The minister was sent on to the BBC’s Today programme instead of Heaton-Harris, who has so far not explained his actions in public other than to tweet in support of both academic freedom and a vigorous debate on Brexit.

Johnson claimed that Heaton-Harris, a longstanding Eurosceptic, had requested a list of tutors and their syllabuses because he was interested in the evolution and history of European thought in a personal capacity.

“Chris has got a very longstanding interest in European affairs and the history of European thought,” Johnson said. “He – I’ve spoken to him – was pursuing inquiries of his own that may in time lead to a book on these questions. It was more of an academic inquiry rather than an attempt to constrain the freedom that academics rightly have.”

Johnson said he was sure Heaton-Harris was “regretting this very much” and “probably didn’t appreciate the extent to which it would be misinterpreted”.

Pressed for a fourth time, he said: “I think Chris doubtless is better placed to speak on this question. I think a letter that could have been misinterpreted should probably not have been sent in this way.”

He did not condemn Heaton-Harris’s conduct, and rebuked the whip’s critics, including Chris Patten, the chancellor of Oxford University, who called the letter an “extraordinary example of outrageous and foolish behaviour – offensive and idiotic Leninism”.

Johnson said that “to describe this as Leninism is a gross exaggeration” as Heaton-Harris was “of course not pursuing any project of political reeducation to dispel false consciousness in our universities”.

“The government is committed to academic freedom. Academics must be free to put together their courses in the way that they see fit. The government can’t interfere in the manner in which they are taught, in the manner in which they are supervised or the manner in which they are assessed.

“We have absolutely no intention of interfering with that, nor do we have any intention of interfering with the criteria of selection of academic staff, their appointment or reasons for dismissal. These are autonomous and private institutions, largely, and we are deeply respectful of that.”

The Lib Dem leader, Vince Cable, said in response that it was a “sign of the weakness of this government that Jo Johnson has been sent out to defend the indefensible”.

“The universities minister should have wasted no time calling out this divisive and fundamentally illiberal attempt to put pressure on academics over Brexit,” he said.

“Instead he came up with excuses that raise more questions than answers. Trying to dismiss this as research simply won’t wash with the many academics who have been made to feel like victims of a witch-hunt.

“University vice-chancellors need to be reassured that this letter was utterly unacceptable and that Chris Heaton-Harris will lose the government whip.

“Anything short of a complete and unequivocal statement on this from the prime minister will simply not do.”